+Open data
-Basic information
Entry | Database: PDB / ID: 3b7b | ||||||
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Title | EuHMT1 (Glp) Ankyrin Repeat Domain (Structure 1) | ||||||
Components | Euchromatic histone-lysine N-methyltransferase 1 | ||||||
Keywords | TRANSFERASE / Ankyrin repeat / Alternative splicing / ANK repeat / Chromatin regulator / Methyltransferase / Nucleus / Phosphorylation / Polymorphism / S-adenosyl-L-methionine | ||||||
Function / homology | Function and homology information [histone H3]-lysine9 N-methyltransferase / histone H3K27 methyltransferase activity / peptidyl-lysine monomethylation / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / peptidyl-lysine dimethylation / protein-lysine N-methyltransferase activity / DNA methylation-dependent heterochromatin formation / C2H2 zinc finger domain binding / Transcriptional Regulation by E2F6 ...[histone H3]-lysine9 N-methyltransferase / histone H3K27 methyltransferase activity / peptidyl-lysine monomethylation / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / peptidyl-lysine dimethylation / protein-lysine N-methyltransferase activity / DNA methylation-dependent heterochromatin formation / C2H2 zinc finger domain binding / Transcriptional Regulation by E2F6 / regulation of embryonic development / Transcriptional Regulation by VENTX / response to fungicide / Transferases; Transferring one-carbon groups; Methyltransferases / transcription corepressor binding / methyltransferase activity / Regulation of TP53 Activity through Methylation / PKMTs methylate histone lysines / p53 binding / positive regulation of cold-induced thermogenesis / chromatin organization / Senescence-Associated Secretory Phenotype (SASP) / nuclear body / negative regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å | ||||||
Authors | Collins, R.E. / Horton, J.R. / Cheng, X. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2008 Title: The ankyrin repeats of G9a and GLP histone methyltransferases are mono- and dimethyllysine binding modules Authors: Collins, R.E. / Northrop, J.P. / Horton, J.R. / Lee, D.Y. / Zhang, X. / Stallcup, M.R. / Cheng, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3b7b.cif.gz | 97.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b7b.ent.gz | 75.5 KB | Display | PDB format |
PDBx/mmJSON format | 3b7b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/3b7b ftp://data.pdbj.org/pub/pdb/validation_reports/b7/3b7b | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 26175.650 Da / Num. of mol.: 2 / Fragment: Ankyrin repeat domains 2-7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EHMT1, EUHMTASE1, KIAA1876 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) CodonPlus References: UniProt: Q9H9B1, histone-lysine N-methyltransferase #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.51 Å3/Da / Density % sol: 64.93 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 1.5-2.0 M Lithium Sulfate, 1-4% Peg 400 or 550, 0.1 M Tris buffer pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97625 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 12, 2007 |
Radiation | Monochromator: Si (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.99→28.75 Å / Num. all: 16000 / Num. obs: 15965 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 11.9 % / Biso Wilson estimate: 32.5 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.99→3.1 Å / Redundancy: 11 % / Rmerge(I) obs: 0.535 / Num. unique all: 1564 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Generated Model from Phyre server Resolution: 2.99→28.75 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 47.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.99→28.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.99→3.1 Å / Rfactor Rfree error: 0.049
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